# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 23:35:47 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: (2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](CC(=O)NO)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 2HM  2HM  '(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoic acid'  peptide  28  13  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2HM
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 2HM  C11   C  CH2   0  -0.565  -0.8011   1.3151   0.6416
 2HM  C21   C  C     0   0.504  -2.1581   1.0286   0.0384
 2HM  O21   O  O     0  -0.472  -2.4520   1.3328  -1.1043
 2HM  N3    N  NH1   0  -0.364  -2.9792   0.3543   0.8635
 2HM  O3    O  OH1   0  -0.542  -4.2763   0.1393   0.5122
 2HM  C     C  C     0   0.542   0.0639  -0.9454   0.0926
 2HM  O     O  O     0  -0.440   0.0252  -1.4982   1.1645
 2HM  C2    C  CH1   0  -0.369   0.3096   0.5380  -0.0773
 2HM  C3    C  CH2   0  -0.397   1.6751   0.9174   0.5031
 2HM  C4    C  CH1   0  -0.252   2.8794   0.2050  -0.1154
 2HM  C5    C  CH3   0  -0.657   3.0102   0.4741  -1.6107
 2HM  CM4   C  CH3   0  -0.650   4.1503   0.6220   0.6183
 2HM  H12   H  HCH2  0   0.290  -0.6089   2.3842   0.5288
 2HM  H13   H  HCH2  0   0.263  -0.7702   1.0976   1.7114
 2HM  HN    H  HNH1  0   0.417  -2.7800   0.2311   1.8456
 2HM  HO    H  HOH1  0   0.479  -4.3131  -0.7539   0.1465
 2HM  H22   H  HCH1  0   0.277   0.2759   0.7920  -1.1383
 2HM  H31   H  HCH2  0   0.236   1.7967   1.9988   0.3803
 2HM  H32   H  HCH2  0   0.235   1.6629   0.7323   1.5815
 2HM  H4    H  HCH1  0   0.223   2.7583  -0.8756   0.0291
 2HM  H51   H  HCH3  0   0.227   2.1462   0.1209  -2.1747
 2HM  H52   H  HCH3  0   0.216   3.1199   1.5438  -1.8042
 2HM  H53   H  HCH3  0   0.230   3.8897  -0.0275  -2.0177
 2HM  HM41  H  HCH3  0   0.227   4.0859   0.3990   1.6845
 2HM  HM42  H  HCH3  0   0.228   5.0237   0.1034   0.2201
 2HM  HM43  H  HCH3  0   0.216   4.3256   1.6956   0.5138
 2HM  HXT   H  HOH1  0   0.480  -0.2663  -2.5224  -0.8985
 2HM  OXT   O  OH1   0  -0.583  -0.1152  -1.5779  -1.0586

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 2HM  C    O     double  1.231  0.020  1.231
 2HM  C    C2    single  1.513  0.020  1.513
 2HM  C2   C3    single  1.531  0.020  1.531
 2HM  C2   H22   single  0.970  0.020  1.090
 2HM  C3   C4    single  1.530  0.020  1.530
 2HM  C3   H31   single  0.970  0.020  1.090
 2HM  C3   H32   single  0.970  0.020  1.090
 2HM  C4   C5    single  1.525  0.020  1.525
 2HM  C4   CM4   single  1.526  0.020  1.526
 2HM  C4   H4    single  0.970  0.020  1.090
 2HM  C5   H51   single  0.970  0.020  1.090
 2HM  C5   H52   single  0.970  0.020  1.090
 2HM  C5   H53   single  0.970  0.020  1.090
 2HM  CM4  HM41  single  0.970  0.020  1.090
 2HM  CM4  HM42  single  0.970  0.020  1.090
 2HM  CM4  HM43  single  0.970  0.020  1.090
 2HM  C11  C21   single  1.512  0.020  1.512
 2HM  C11  H12   single  0.970  0.020  1.090
 2HM  C11  H13   single  0.970  0.020  1.090
 2HM  C21  O21   double  1.218  0.020  1.218
 2HM  C21  N3    single  1.345  0.020  1.345
 2HM  N3   O3    single  1.361  0.020  1.361
 2HM  N3   HN    single  0.860  0.020  1.020
 2HM  O3   HO    single  0.850  0.020  0.980
 2HM  C2   C11   single  1.534  0.020  1.534
 2HM  C    OXT   single  1.326  0.020  1.326
 2HM  OXT  HXT   single  0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 2HM  H13   C11  H12   106.93  3.000
 2HM  H13   C11  C2    109.73  3.000
 2HM  H12   C11  C2    108.66  3.000
 2HM  C2    C11  C21   111.51  3.000
 2HM  H13   C11  C21   112.24  3.000
 2HM  H12   C11  C21   107.59  3.000
 2HM  N3    C21  O21   123.59  3.000
 2HM  N3    C21  C11   113.45  3.000
 2HM  O21   C21  C11   122.90  3.000
 2HM  HN    N3   O3    114.83  3.000
 2HM  HN    N3   C21   122.51  3.000
 2HM  O3    N3   C21   120.17  3.000
 2HM  HO    O3   N3    106.27  3.000
 2HM  OXT   C    C2    113.09  3.000
 2HM  OXT   C    O     123.26  3.000
 2HM  C2    C    O     123.65  3.000
 2HM  H22   C2   C3    109.77  3.000
 2HM  H22   C2   C     109.40  3.000
 2HM  C3    C2   C     110.19  3.000
 2HM  H22   C2   C11   108.38  3.000
 2HM  C3    C2   C11   110.03  3.000
 2HM  C     C2   C11   109.05  3.000
 2HM  H32   C3   H31   106.18  3.000
 2HM  H32   C3   C4    109.18  3.000
 2HM  H31   C3   C4    109.09  3.000
 2HM  H32   C3   C2    108.76  3.000
 2HM  H31   C3   C2    107.52  3.000
 2HM  C4    C3   C2    115.68  3.000
 2HM  H4    C4   CM4   107.33  3.000
 2HM  H4    C4   C5    108.21  3.000
 2HM  CM4   C4   C5    110.60  3.000
 2HM  H4    C4   C3    108.58  3.000
 2HM  CM4   C4   C3    109.52  3.000
 2HM  C5    C4   C3    112.44  3.000
 2HM  H53   C5   H52   107.64  3.000
 2HM  H53   C5   H51   107.27  3.000
 2HM  H52   C5   H51   107.76  3.000
 2HM  H53   C5   C4    110.71  3.000
 2HM  H52   C5   C4    110.79  3.000
 2HM  H51   C5   C4    112.46  3.000
 2HM  HM43  CM4  HM42  107.68  3.000
 2HM  HM43  CM4  HM41  107.68  3.000
 2HM  HM42  CM4  HM41  107.86  3.000
 2HM  HM43  CM4  C4    110.87  3.000
 2HM  HM42  CM4  C4    111.19  3.000
 2HM  HM41  CM4  C4    111.40  3.000
 2HM  HXT   OXT  C     110.02  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 2HM  CONST_01  O3    N3   C21  C11  180.00   0.0  0
 2HM  CONST_02  O3    N3   C21  O21    0.00   0.0  0
 2HM  CONST_03  HN    N3   C21  C11    0.00   0.0  0
 2HM  CONST_04  HXT   OXT  C    O      0.00   0.0  0
 2HM  Var_01    C2    C11  C21  O21  -64.40  30.0  1
 2HM  Var_02    C5    C4   C3   C2    59.97  30.0  3
 2HM  Var_03    H51   C5   C4   C3   -61.34  30.0  3
 2HM  Var_04    HM41  CM4  C4   C3    57.76  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2HM  chir_01  C2  C  C3  C11  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 2HM  plan-1  C11  0.020
 2HM  plan-1  C21  0.020
 2HM  plan-1  O21  0.020
 2HM  plan-1  N3   0.020
 2HM  plan-1  O3   0.020
 2HM  plan-1  HN   0.020
 2HM  plan-2  C    0.020
 2HM  plan-2  O    0.020
 2HM  plan-2  C2   0.020
 2HM  plan-2  HXT  0.020
 2HM  plan-2  OXT  0.020

